5QTY

FACTOR XIA IN COMPLEX WITH THE INHIBITOR ethyl (2R,7S)-7-({(2E)-3-[5-chloro-2-(1H-tetrazol-1-yl)phenyl]prop-2-enoyl}amino)-15-[(methoxycarbonyl)amino]-2,3,4,5,6,7-hexahydro-1H-12,8-(metheno)-1,9-benzodiazacyclotetradecine-2-carboxylate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.155 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

Orally bioavailable amine-linked macrocyclic inhibitors of factor XIa.

Fang, T., Corte, J.R., Gilligan, P.J., Jeon, Y., Osuna, H., Rossi, K.A., Myers Jr., J.E., Sheriff, S., Lou, Z., Zheng, J.J., Harper, T.W., Bozarth, J.M., Wu, Y., Luettgen, J.M., Seiffert, D.A., Wexler, R.R., Lam, P.Y.S.

(2020) Bioorg Med Chem Lett 30: 126949-126949

  • DOI: https://doi.org/10.1016/j.bmcl.2020.126949
  • Primary Citation of Related Structures:  
    5QTV, 5QTW, 5QTX, 5QTY

  • PubMed Abstract: 

    • The discovery of orally bioavailable FXIa inhibitors has been a challenge. Herein, we describe our efforts to address this challenge by optimization of our imidazole-based macrocyclic series. Our optimization strategy focused on modifications to the P2 prime, macrocyclic amide linker, and the imidazole scaffold ...

    The discovery of orally bioavailable FXIa inhibitors has been a challenge. Herein, we describe our efforts to address this challenge by optimization of our imidazole-based macrocyclic series. Our optimization strategy focused on modifications to the P2 prime, macrocyclic amide linker, and the imidazole scaffold. Replacing the amide of the macrocyclic linker with amide isosteres led to the discovery of substituted amine linkers which not only maintained FXIa binding affinity but also improved oral exposure in rats. Combining the optimized macrocyclic amine linker with a pyridine scaffold afforded compounds 23 and 24 that were orally bioavailable, single-digit nanomolar FXIa inhibitors with excellent selectivity against relevant blood coagulation enzymes.

    Related Citations: 
    • Tetrahydroquinoline derivatives as potent and selective factor XIa inhibitors.
      Quan, M.L., Wong, P.C., Wang, C., Woerner, F., Smallheer, J.M., Barbera, F.A., Bozarth, J.M., Brown, R.L., Harpel, M.R., Luettgen, J.M., Morin, P.E., Peterson, T., Ramamurthy, V., Rendina, A.R., Rossi, K.A., Watson, C.A., Wei, A., Zhang, G., Seiffert, D., Wexler, R.R.
      (2014) J Med Chem 57: 955
    • Phenylimidazoles as potent and selective inhibitors of coagulation factor XIa with in vivo antithrombotic activity.
      Hangeland, J.J., Friends, T.J., Rossi, K.A., Smallheer, J.M., Wang, C., Sun, Z., Corte, J.R., Fang, T., Wong, P.C., Rendina, A.R., Barbera, F.A., Bozarth, J.M., Luettgen, J.M., Watson, C.A., Zhang, G., Wei, A., Ramamurthy, V., Morin, P.E., Bisacchi, G.S., Subramaniam, S., Arunachalam, P., Mathur, A., Seiffert, D.A., Wexler, R.R., Quan, M.L.
      (2014) J Med Chem 57: 9915
    • Pyridine and pyridinone-based factor XIa inhibitors.
      Corte, J.R., Fang, T., Hangeland, J.J., Friends, T.J., Rendina, A.R., Luettgen, J.M., Bozarth, J.M., Barbera, F.A., Rossi, K.A., Wei, A., Ramamurthy, V., Morin, P.E., Seiffert, D.A., Wexler, R.R., Quan, M.L.
      (2015) Bioorg Med Chem Lett 25: 925
    • Structure-based design of inhibitors of coagulation factor XIa with novel P1 moieties.
      Pinto, D.J., Smallheer, J.M., Corte, J.R., Austin, E.J., Wang, C., Fang, T., Smith 2nd., L.M., Rossi, K.A., Rendina, A.R., Bozarth, J.M., Zhang, G., Wei, A., Ramamurthy, V., Sheriff, S., Myers Jr., J.E., Morin, P.E., Luettgen, J.M., Seiffert, D.A., Quan, M.L., Wexler, R.R.
      (2015) Bioorg Med Chem Lett 25: 1635
    • Discovery of a Potent Parenterally Administered Factor XIa Inhibitor with Hydroxyquinolin-2(1H)-one as the P2' Moiety.
      Hu, Z., Wong, P.C., Gilligan, P.J., Han, W., Pabbisetty, K.B., Bozarth, J.M., Crain, E.J., Harper, T., Luettgen, J.M., Myers Jr., J.E., Ramamurthy, V., Rossi, K.A., Sheriff, S., Watson, C.A., Wei, A., Zheng, J.J., Seiffert, D.A., Wexler, R.R., Quan, M.L.
      (2015) ACS Med Chem Lett 6: 590
    • Novel phenylalanine derived diamides as Factor XIa inhibitors.
      Smith 2nd., L.M., Orwat, M.J., Hu, Z., Han, W., Wang, C., Rossi, K.A., Gilligan, P.J., Pabbisetty, K.B., Osuna, H., Corte, J.R., Rendina, A.R., Luettgen, J.M., Wong, P.C., Narayanan, R., Harper, T.W., Bozarth, J.M., Crain, E.J., Wei, A., Ramamurthy, V., Morin, P.E., Xin, B., Zheng, J., Seiffert, D.A., Quan, M.L., Lam, P.Y.S., Wexler, R.R., Pinto, D.J.P.
      (2016) Bioorg Med Chem Lett 26: 472
    • Orally bioavailable pyridine and pyrimidine-based Factor XIa inhibitors: Discovery of the methyl N-phenyl carbamate P2 prime group.
      Corte, J.R., Fang, T., Pinto, D.J., Orwat, M.J., Rendina, A.R., Luettgen, J.M., Rossi, K.A., Wei, A., Ramamurthy, V., Myers Jr., J.E., Sheriff, S., Narayanan, R., Harper, T.W., Zheng, J.J., Li, Y.X., Seiffert, D.A., Wexler, R.R., Quan, M.L.
      (2016) Bioorg Med Chem 24: 2257
    • Structure-Based Design of Macrocyclic Factor XIa Inhibitors: Discovery of the Macrocyclic Amide Linker.
      Corte, J.R., Fang, T., Osuna, H., Pinto, D.J., Rossi, K.A., Myers Jr., J.E., Sheriff, S., Lou, Z., Zheng, J.J., Harper, T.W., Bozarth, J.M., Wu, Y., Luettgen, J.M., Seiffert, D.A., Decicco, C.P., Wexler, R.R., Quan, M.L.
      (2017) J Med Chem 60: 1060
    • Macrocyclic inhibitors of Factor XIa: Discovery of alkyl-substituted macrocyclic amide linkers with improved potency.
      Corte, J.R., Yang, W., Fang, T., Wang, Y., Osuna, H., Lai, A., Ewing, W.R., Rossi, K.A., Myers Jr., J.E., Sheriff, S., Lou, Z., Zheng, J.J., Harper, T.W., Bozarth, J.M., Wu, Y., Luettgen, J.M., Seiffert, D.A., Quan, M.L., Wexler, R.R., Lam, P.Y.S.
      (2017) Bioorg Med Chem Lett 27: 3833
    • Macrocyclic factor XIa inhibitors.
      Wang, C., Corte, J.R., Rossi, K.A., Bozarth, J.M., Wu, Y., Sheriff, S., Myers Jr., J.E., Luettgen, J.M., Seiffert, D.A., Wexler, R.R., Quan, M.L.
      (2017) Bioorg Med Chem Lett 27: 4056
    • Discovery of a Parenteral Small Molecule Coagulation Factor XIa Inhibitor Clinical Candidate (BMS-962212).
      Pinto, D.J.P., Orwat, M.J., Smith 2nd., L.M., Quan, M.L., Lam, P.Y.S., Rossi, K.A., Apedo, A., Bozarth, J.M., Wu, Y., Zheng, J.J., Xin, B., Toussaint, N., Stetsko, P., Gudmundsson, O., Maxwell, B., Crain, E.J., Wong, P.C., Lou, Z., Harper, T.W., Chacko, S.A., Myers Jr., J.E., Sheriff, S., Zhang, H., Hou, X., Mathur, A., Seiffert, D.A., Wexler, R.R., Luettgen, J.M., Ewing, W.R.
      (2017) J Med Chem 60: 9703
    • Structure based design of macrocyclic factor XIa inhibitors: Discovery of cyclic P1 linker moieties with improved oral bioavailability.
      Clark, C.G., Rossi, K.A., Corte, J.R., Fang, T., Smallheer, J.M., De Lucca, I., Nirschl, D.S., Orwat, M.J., Pinto, D.J.P., Hu, Z., Wang, Y., Yang, W., Jeon, Y., Ewing, W.R., Myers Jr., J.E., Sheriff, S., Lou, Z., Bozarth, J.M., Wu, Y., Rendina, A., Harper, T., Zheng, J., Xin, B., Xiang, Q., Luettgen, J.M., Seiffert, D.A., Wexler, R.R., Lam, P.Y.S.
      (2019) Bioorg Med Chem Lett 29: 126604
    • Potent, Orally Bioavailable, and Efficacious Macrocyclic Inhibitors of Factor XIa. Discovery of Pyridine-Based Macrocycles Possessing Phenylazole Carboxamide P1 Groups.
      Corte, J.R., Pinto, D.J.P., Fang, T., Osuna, H., Yang, W., Wang, Y., Lai, A., Clark, C.G., Sun, J.H., Rampulla, R., Mathur, A., Kaspady, M., Neithnadka, P.R., Li, Y.C., Rossi, K.A., Myers Jr., J.E., Sheriff, S., Lou, Z., Harper, T.W., Huang, C., Zheng, J.J., Bozarth, J.M., Wu, Y., Wong, P.C., Crain, E.J., Seiffert, D.A., Luettgen, J.M., Lam, P.Y.S., Wexler, R.R., Ewing, W.R.
      (2020) J Med Chem 63: 784
    Organizational Affiliation: 

    Bristol-Myers Squibb Company, Research and Development, 350 Carter Road, Hopewell, NJ 08540, United States.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor XI244Homo sapiensMutation(s): 0 
Gene Names: F11
EC: 3.4.21.27
UniProt & NIH Common Fund Data Resources
Find proteins for P03951 (Homo sapiens)
Explore P03951 
Go to UniProtKB:  P03951
PHAROS:  P03951
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03951
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QLJ
Query on QLJ
Download Ideal Coordinates CCD File 
B [auth A]ethyl (2R,7S)-7-({(2E)-3-[5-chloro-2-(1H-tetrazol-1-yl)phenyl]prop-2-enoyl}amino)-15-[(methoxycarbonyl)amino]-2,3,4,5,6,7-hexahydro-1H-12,8-(metheno)-1,9-benzodiazacyclotetradecine-2-carboxylate
C32 H33 Cl N8 O5
SBASSQZHYOTWFU-RXPDHRDVSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
QLJ Binding MOAD:  5QTY Ki: 2.5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.155 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.53α = 90
b = 78.53β = 90
c = 105.95γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
AMoREphasing
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

  • Released Date: 2020-01-29 
    • Deposition Author(s): Sheriff, S.

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-29
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Data collection, Database references
  • Version 1.2: 2020-03-18
    Changes: Data collection, Database references
  • Version 1.3: 2021-05-12
    Changes: Structure summary